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. 2010 Feb 3;5(2):e9007.
doi: 10.1371/journal.pone.0009007.

Large Direct Repeats Flank Genomic Rearrangements Between a New Clinical Isolate of Francisella Tularensis Subsp. Tularensis A1 and Schu S4

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Free PMC article

Large Direct Repeats Flank Genomic Rearrangements Between a New Clinical Isolate of Francisella Tularensis Subsp. Tularensis A1 and Schu S4

Ufuk Nalbantoglu et al. PLoS One. .
Free PMC article

Abstract

Francisella tularensis subspecies tularensis consists of two separate populations A1 and A2. This report describes the complete genome sequence of NE061598, an F. tularensis subspecies tularensis A1 isolated in 1998 from a human with clinical disease in Nebraska, United States of America. The genome sequence was compared to Schu S4, an F. tularensis subspecies tularensis A1a strain originally isolated in Ohio in 1941. It was determined that there were 25 nucleotide polymorphisms (22 SNPs and 3 indels) between Schu S4 and NE061598; two of these polymorphisms were in potential virulence loci. Pulsed-field gel electrophoresis analysis demonstrated that NE061598 was an A1a genotype. Other differences included repeat sequences (n = 11 separate loci), four of which were contained in coding sequences, and an inversion and rearrangement probably mediated by insertion sequences and the previously identified direct repeats I, II, and III. Five new variable-number tandem repeats were identified; three of these five were unique in NE061598 compared to Schu S4. Importantly, there was no gene loss or gain identified between NE061598 and Schu S4. Interpretation of these data suggests there is significant sequence conservation and chromosomal synteny within the A1 population. Further studies are needed to determine the biological properties driving the selective pressure that maintains the chromosomal structure of this monomorphic pathogen.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Figure 1
Figure 1. Genome rearrangement representation for NE061598 and Schu S4 genomes.
Each local collinear blocks (LCB) 1-6 is represented by a different color. Upside-down blocks (i.e. LCB2) represent the location of the reverse strand, which means an inversion has occurred. Note the rearrangements of LCB4 and LCB5.
Figure 2
Figure 2. Depiction of genomic rearrangement between local collinear blocks 4 and 5 in NE061598 compared to Schu S4.
Direct repeats 1 (DRI) and II (DRII) are colored in green in both 3A (Schu S4) and 3B (NE061598). DRIII, a segment of both DRI and DRII, is colored in red. Note that DRIII is found independently in LCB4. The initial 207 bp of DRI and DRII in Schu S4 is colored in blue. Note that the genomic rearrangement resulted in the loss of this initial 207 bp region in DR1 of NE061598.
Figure 3
Figure 3. Genome rearrangement representation for NE061598, Schu S4 and FSC033 genomes.
Each local collinear blocks (LCB) 1–10 is represented by a different color. Upside-down blocks (i.e. LCBs 3 and 9) represent the location of the reverse strand, which means an inversion has occurred. Each LCB is denoted above NE061598.

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